Fundamental of Data Science for EESS

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# Fundamentals of Data Science for EESS

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## R session 02 - R markdown

2020-01-24

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# Outline

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# Installation and Resources

* rmarkdown (will install also knitr)
* tinytex (Latex)

## Resources
* On-line Book: https://bookdown.org/yihui/rmarkdown

* Cheat sheet: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf
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<img src="img/R-markdown-book.png" width="65%" style="display: block; margin: auto;" />
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# What is markdown ?

.center[
<img src="img/markdown-John_Gruber.jpg" width="20%" /><img src="img/markdown-Aaron_Swartz.jpg" width="20%" />
]

* Created in 2004 by [John Gruber](https://en.wikipedia.org/wiki/John_Gruber) and [Aaron Swartz](https://en.wikipedia.org/wiki/Aaron_Swartz)

* Goal : "to write using an easy-to-read and easy-to-write plain text format, optionally convert it to structurally valid HTML".

## Many flavors...

* MultiMarkdown
* GitHub Flavored Markdown (GFM)
* Pandoc
* CommonMark

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# Rmarkdown

## Mix

* Markdown
    - paragraph structure
    - comments
    - links

* R code ("chunks")

* Output of R code

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# Your first Rmarkdown file

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.student[Who has not been able to install Rmarkdown and Latex ?]

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![](img/R-markdown_new.gif)

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## Knit to HTML

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## Knit of pdf

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<img src="img/package-rmarkdown-pdf-output.png" width="100%" />

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# Markdown syntax

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* Quick guide: https://www.markdownguide.org/basic-syntax/

## Headings

```r
# Heading - level 1

## Heading - level 2
```
--
 
## Heading - level 1
 
### Heading - level 2

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## Paragraphs

```r
Paragraphs are separated
by a blank line.

Two spaces at the end of a line  
produces a line break.
```
--

Paragraphs are separated
by a blank line.

Two spaces at the end of a line  
produces a line break.

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## Formatting

```r
_italic_, *italic*, **bold**, `monospace`.
```

_italic_, *italic*, **bold**, `monospace`.

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## Bullet lists

```r
Bullet list:

* apples
  * oranges
  * pears
      * passe crassane (4 spaces to indent)
```

* apples
* oranges
* pears
    * passe crassane

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## Numbered lists

```r
Numbered list:

1. wash
1. rinse
1. repeat
```
--

1. wash
1. rinse
1. repeat

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## Hyperlinks

```r
  [Text of the link](URL of the link)

# Example
  [Markdown syntax](https://www.markdownguide.org/basic-syntax/)
```

[Markdown syntax](https://www.markdownguide.org/basic-syntax/)

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## Images

```r
  ![Image name](URL of the link - can also be a local file on your computer)

# Example
  ![](https://i.pinimg.com/originals/1c/b7/24/1cb724b545de717ed0430e9d46e78eea.jpg)
```

![](https://i.pinimg.com/originals/1c/b7/24/1cb724b545de717ed0430e9d46e78eea.jpg)

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## Tables

```r
ID | First | Last
--- | --- | ---
1 | Donald | Trump
```

ID | First | Last
--- | --- | ---
1 | Donald | Trump

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# Rmarkdown conversion

* [Pandoc](https://pandoc.org/) : command line tool

* Converts from **md** to **pdf**, **html**, **docx**...

```r
# HTML
> pandoc test1.md -f markdown -t html -s -o test1.html

# pdf
> pandoc test1.md -s -o test1.pdf
```
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<img src="img/pandoc.png" width="100%" style="display: block; margin: auto auto auto 0;" />
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# The Rmarkdown file

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## File structure

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## Knit process

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## Output

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# R Chunks

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## Insert R chunk

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## Run R chunk

* Two options

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## Option 1: Run R chunk inside Rmd file

- Use when building and debugging an Rmd file

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## Option 2: Knit R chunk to HTML

- Use for final production

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## Options for R chunks

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exclude: false

## Useful options

Options | Default value | Aim
--- | --- | ---
echo | TRUE | Print code (= FALSE in a report for example)
eval | TRUE | Evaluate code (= FALSE if want to show code only)
warning  | TRUE | Warning message (= FALSE to remove long warnings)
message  | TRUE | Messages (= FALSE to remove long messages)
cache   | FALSE | If TRUE only modified chunks will be evaluated
   |  |  very useful for computing heavy codes
fig.height  |  |  inches
fig.width  |  |  inches

---
exclude: false

## Set defaults options

* Insert in a R chunk at the beginning of your Rmarkdown file
* Option CACHE = true reduce compiling time

```r
  knitr::opts_chunk$set(fig.width=6, fig.height=6, 
                        eval=TRUE, 
                        cache=TRUE,
                        echo=TRUE,)
```

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# What can you do with Rmarkdown ?

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## Document your data analyses

* If the data changes, you can re-run analysis in a matter of minutes
* More and more journal request analyses scripts

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## Presentation

https://github.com/yihui/xaringan

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## Posters

.left-column[
<img src="img/package-posterdown-logo.png" width="60%" />
https://github.com/brentthorne/posterdown
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## Curriculum vitae

https://cloud.r-project.org/web/packages/vitae/index.html
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## Website

https://bookdown.org/yihui/blogdown/
 
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# What did you learn ?

--
.font150[
- Can be used for many different purposes
]

--
.font150[
- Use to document your analysis process (for papers...)
]